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Evolution

Carnival of Evolution, February 2014 Edition

Wow, I haven’t posted anything in quite a while. Things are busy outside blogoland. But committing this blog to the February edition of the Carnival of Evolution just made me do it, so here goes. We’ll do this by scales, bottom up. Molecular Prions are the infective agents that cause transmissible spongiform encephalopathies such as […]

Bats use blood to reshape tongue for feeding

Great bit of research showing the amazing adaptation of bat tongues to nectar feeding.   Harper, C., Swartz, S., & Brainerd, E. (2013). Specialized bat tongue is a hemodynamic nectar mop Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.1222726110  

The Black Queen Hypothesis

“Well, in our country,” said Alice, still panting a little, “you’d generally get to somewhere else — if you run very fast for a long time, as we’ve been doing.” “A slow sort of country!” said the Queen. “Now, here, you see, it takes all the running you can do, to keep in the same […]

DNA half life, and my dream of an Allosaurus Army

Let’s get this clear: Tyrannosaurus rex, the best selling figurine of class reptilia is not my favorite bad-ass top-of-the-food chain predator. Come on. Did you see its arms? I mean…   As a kid, I always thought the Allosaurus was much cooler. For one thing, it was on the cover of my favorite dinosaur book, “The […]

Repost: the New Natural History

Today is the last day of the 19th Lake Arrowhead Microbial Genomics meeting. A great meeting of everything good: science, atmosphere, people and location. Good tweeter coverage too, at #LAMG12 The many genomic characterization talks in the meeting reminded me of a post I wrote three years ago. I decided to repost it, and dedicate […]

ISMB 2012 Vignettes Pt. 3: Swag

Promotional materials are part of any conference. In scientific meetings, the swag usually comes from the booths of product promoters, science publishers, and scientific societies. It was a nice surprise to see a Federal funding agency, the US Department of Energy give away decks of cards. I’m a sucker for cards, so I took a […]

ISMB 2012 Vignettes Pt. 2: Phylogenomic Approaches to Function Prediction

I chaired the Automated Function Prediction meeting at ISMB this year. The meeting, held every year (almost) deals with the latest approaches to predicting protein function from genetic and genomic data, and also discussing the Critical Assessment of Function Annotation This year we were fortunate to have Jonathan Eisen as our keynote speaker. Ever wondered […]

The Evolution of Music

A collaboration between a group in  Imperial College and Media Interaction group in Japan yielded a really cool website: darwintunes.org. The idea is to  apply Darwinian-like selection to music. Starting form a garble, after several generations producing  something that is actually melodic and listen-able. Or a Katy Perry tune. Whatever.  The selective force being the appeal of […]

Repost: the Scope(s) of Substance

This tweet from Neil Degrasse Tyson jolted me from a pleasant rest before tomorrow’s race:   …which led to the (in)famous Scopes Trial. On May 5, 1925 John Scopes was charged and subsequently tried, found guilty, and fined $100 for teaching Evolution, a violation of Tennessee’s Butler Act. The trial became a battleground for science […]

It’s a smORF world, after all?

Here is a study that looked for a type of genes that the authors felt was neglected by classic genomic annotation. The research shows how to employed concepts in molecular evolution to validate the existence of these genes. Some background: the first question we ask after assembling a genome is: “where are the genes”? Not […]

The Friedberg Lab is Recruiting Graduate Students

  The Friedberg Lab is recruiting graduate students, for both Master’s and Ph.D. WE ARE:  A dynamic young lab  interested in gene, gene cluster and genome evolution, understanding microbial communities and microbe-host interactions by metagenomic analyses, developing algorithms for understanding gene cluster evolution, and prediction of protein function from protein sequence and structure. YOU ARE: […]

The power of science blogging

  Hats off to Jonathan Eisen for hosting this activity on his blog. (I’ll keep mine on, thank you. It’s raining cats and dogs here right now). A couple of weeks ago I posted a discussion about two papers that challenged the ortholog conjecture. Briefly, both papers stated that orthologs may not be such great […]

Of Mice and Men or: Revisiting the Ortholog Conjecture

I  have posted quite a few times before about the acquisition of new functions by genes. In many cases a gene is duplicated, and one of the duplicates acquires a new function. This is one basic evolutionary mechanism of acquiring new functions. Sometimes, gene duplication occurs within a species: part of the chromosome may be […]

Zombie science roundup

  I am fascinated with zombies. Always have been, but even more so since I took an interest in microbiology. The zombie apocalypse is the best known and best chronicled viral infection which hasn’t happened. But it could happen any day, so stock up on non-perishable food, medical supplies, water purification tablets, chainsaws, machetes, baseball […]

Life is not a tree, it’s more of a…

  OK, I think the tree of life is obsolete. I have been spending a lot of time looking at horizontal gene transfer, reading about it, looking at it in genomes until my eyes water and my brain dessicates, occasionally blogging about it and soon to be publishing about it. Life is not a tree. […]